Hi Mark,
Thanks for posting your code. Following exactly what you did(the same
code and the same custom CDF), I can reproduce what you got.
However, next I put the version 10 of the U133A Refseq custom CDF
(binary file) into the relevant locations (For version 10, there is
supposed to be 17599 units)
I used the same code.
At the command
fit(plm, verbose=verbose),
I got the error message
"
Fitting chunk #1 of 1...
Units:
int [1:19760] 1 2 3 4 5 6 7 8 9 10 ...
Error in readCdfCellIndices(pathname, ...) :
Argument 'units' contains an element out of range: 17600
Fitting chunk #1 of 1...done
Fitting model of class RmaPlm:...done
"
I then changed fit(plm, verbose=verbose) to fit(plm, units=NULL,
verbose=verbose) and resolved the issue.
Finally the dimension I got is 19760 instead of 17599, which is for
v12 but not for v10
I now remember the "11979" I kept getting before is from some custom
cdf I used earlier.
As I used the same code as yours, I only posted the directory, cdf
infor and sessionInfo from my run
> print(cdf)
AffymetrixCdfFile:
Path: annotationData/chipTypes/HG-U133A
Filename: HG-U133A,Hs_REFSEQ.cdf
Filesize: 10.04MB
Chip type: HG-U133A,Hs_REFSEQ
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 712x712
Number of cells: 506944
Number of units: 17599
Cells per unit: 28.81
Number of QC units: 10
>dir("rawData/test/HG-U133A/")
[1] "GSM65316,.CEL" "GSM65317,.CEL" "GSM65318,.CEL" "GSM65319,.CEL"
R version 2.9.0 (2009-04-17)
i386-apple-darwin8.11.1
> sessionInfo()
locale:
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods
base
other attached packages:
[1] preprocessCore_1.6.0 Biobase_2.4.1
aroma.affymetrix_1.1.1 aroma.apd_0.1.6 affxparser_1.16.0
R.huge_0.1.8 aroma.core_1.1.2 aroma.light_1.12.2
[9] matrixStats_0.1.6 R.rsp_0.3.4
R.filesets_0.5.2 digest_0.3.1 R.cache_0.1.7
R.utils_1.1.7 R.oo_1.4.8 affy_1.22.0
[17] R.methodsS3_1.0.3
loaded via a namespace (and not attached):
[1] affyio_1.12.0
Thanks.
Yiwen
On Aug 14, 3:11 pm, Mark Robinson <mrobin...@wehi.edu.au> wrote:
> Hi Yiwen.
>
> Well, I'm having trouble reproducing this problem. I downloaded
> version 12 of the U133A Refseq custom CDF from:
>
> http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/12...
>
> and converted it to binary using convertCdf(), then put the files in
> the relevant locations. The commands below generate a matrix of chip
> effects with the correct dimensions.
>
> --------------------
> cdf <- AffymetrixCdfFile$fromChipType("HG-U133A",tag="Hs_REFSEQ")
> cs <- AffymetrixCelSet$fromName("test", cdf=cdf)
>
> bc <- RmaBackgroundCorrection(cs);
> csBC <- process(bc, verbose=verbose);
>
> qn <- QuantileNormalization(csBC, typesToUpdate="pm");
> csN <- process(qn, verbose=verbose);
>
> plm <- RmaPlm(csN);
> fit(plm, verbose=verbose);
> ces <- getChipEffectSet(plm)
>
> dm <- extractMatrix(ces)
>
> > dir("rawData/test/HG-U133A/")
>
> [1] "E-TABM-26-raw-cel-518987776.cel" "E-TABM-26-raw-cel-518987804.cel"
>
> [3] "E-TABM-26-raw-cel-518987862.cel" "E-TABM-26-raw-cel-518987878.cel"
>
> > dir("annotationData/chipTypes/HG-U133A/")
>
> [1] "HG-U133A,Hs_REFSEQ,monocell.CDF" "HG-U133A,Hs_REFSEQ.cdf"
>
> > dim(dm)
>
> [1] 19760 4
>
> > print(cdf)
>
> AffymetrixCdfFile:
>
> Path: annotationData/chipTypes/HG-U133A
>
> Filename: HG-U133A,Hs_REFSEQ.cdf
>
> Filesize: 11.32MB
>
> Chip type: HG-U133A,Hs_REFSEQ
>
> RAM: 0.00MB
>
> File format: v4 (binary; XDA)
>
> Dimension: 712x712
>
> Number of cells: 506944
>
> Number of units: 19760
>
> Cells per unit: 25.66
>
> Number of QC units: 10
>
> > sessionInfo()
>
> R version 2.9.1 (2009-06-26)
>
> i386-apple-darwin8.11.1
>
> locale:
>
> en_CA.UTF-8/en_CA.UTF-8/C/C/en_CA.UTF-8/en_CA.UTF-8
>
> attached base packages:
>
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
>
> [1] preprocessCore_1.6.0 Biobase_2.4.1
> aroma.affymetrix_1.1.0
>
> [4] aroma.apd_0.1.6 R.huge_0.1.8 aroma.core_1.1.3
>
> [7] aroma.light_1.13.2 matrixStats_0.1.7 R.rsp_0.3.5
>
> [10] R.filesets_0.5.3 digest_0.3.1 R.cache_0.1.8
>
> [13] R.utils_1.1.7 R.oo_1.4.8 affy_1.22.0
>
> [16] R.methodsS3_1.0.3 affxparser_1.15.6
>
> loaded via a namespace (and not attached):
>
> [1] affyio_1.12.0
>
> --------------------
>
> Perhaps you can attach a complete code example and your sessionInfo().
>
> Cheers,
> Mark
>
> On 15-Aug-09, at 2:04 AM, tea wrote:
>
>
>
>
>
> > To test other possibilities, I modified the following function
> > theta <- extractMatrix(ces, returnUgcMap=TRUE)
> > to
> > theta <- extractMatrix(ces, returnRefcMap=TRUE)
> > It gave the same result.
>
> > On Aug 14, 11:57 am, tea <ywcu...@gmail.com> wrote:
> >> Hi Mark,
>
> >> The following are the outputs:> cdf<- getCdf(cs)
> >>> print(cdf)
>
> >> AffymetrixCdfFile:
> >> Path: annotationData/chipTypes/HG-U133A
> >> Filename: HG-U133A.cdf
> >> Filesize: 41.16MB
> >> Chip type: HG-U133A
> >> RAM: 0.00MB
> >> File format: v3 (text; ASCII)
> >> Dimension: 712x712
> >> Number of cells: 506944
> >> Number of units: 17599
> >> Cells per unit: 28.81
> >> Number of QC units: 10> print(getMonoCell(cdf))
>
> >> AffymetrixCdfFile:
> >> Path: annotationData/chipTypes/HG-U133A
> >> Filename: HG-U133A,monocell.CDF
> >> Filesize: 3.11MB
> >> Chip type: HG-U133A,monocell
> >> RAM: 0.00MB
> >> File format: v4 (binary; XDA)
> >> Dimension: 147x146
> >> Number of cells: 21462
> >> Number of units: 17599
> >> Cells per unit: 1.22
> >> Number of QC units: 10> print(getCdf(ces))
>
> >> AffymetrixCdfFile:
> >> Path: annotationData/chipTypes/HG-U133A
> >> Filename: HG-U133A,monocell.CDF
> >> Filesize: 3.11MB
> >> Chip type: HG-U133A,monocell
> >> RAM: 0.00MB
> >> File format: v4 (binary; XDA)
> >> Dimension: 147x146
> >> Number of cells: 21462
> >> Number of units: 17599
> >> Cells per unit: 1.22
> >> Number of QC units: 10
>
> >> On Aug 14, 1:51 am, Mark Robinson <mrobin...@wehi.edu.au> wrote:
>
> >>> Hi Yiwen.
>
> >>> Can you check a couple quick things for me?
>
> >>> What does the output of these give:
>
> >>> cdf <- getCdf(cs)
>
> >>> print(cdf)
>
> >>> print(getMonoCell(cdf))
>
> >>> print(getCdf(ces))
>
> >>> Cheers,
> >>> Mark
>
> >>> On 14-Aug-09, at 1:44 PM, tea wrote:
>
> >>>> Hi,
>
> >>>> I used the script in the following page:
> >>>>http://groups.google.com/group/aroma-affymetrix/web/redundancy-
> >>>> tests
> >>>> to process a dataset of 189 arrays using Human custom refseq CDF
> >>>> version 10, HGU133A_Hs_REFSEQ
> >>>> After I finished
> >>>> fit(plm, verbose=verbose)
> >>>> I got the following message:
> >>>> "
> >>>> Total time for all units across all 189 arrays: 532.37s == 8.87min
> >>>> Total time per unit across all 189 arrays: 0.04s/unit
> >>>> Total time per unit and array: 0.235ms/unit & array
> >>>> Total time for one array (17599 units): 0.07min = 0.00h
> >>>> "
> >>>> When I finished up to the code
> >>>> ces <- getChipEffectSet(plm);
> >>>> theta <- extractMatrix(ces, returnUgcMap=TRUE);
> >>>> theta <- log2(theta);
> >>>> ugcMap <- attr(theta, "unitGroupCellMap");
> >>>> rownames(theta) <- getUnitNames(getCdf(ces), ugcMap[,"unit"]
> >>>> and type
>
> >>>> dim(theta)
> >>>> I found that he total number of probesets is only 11979.
> >>>> "11979 189"
>
> >>>> If I used affy(rma) and tested on a small number of CEL file from
> >>>> the
> >>>> same dataset, the total number of probesets is 17599.
>
> >>>> From the custom cdf document the total number of probeset of this
> >>>> cdf
> >>>> is 17531, so with the "AFFX" probes(68),
> >>>> the total number should be 17599. I was wondering what parameter
> >>>> should be used to get right number of probesets from cdf file for
> >>>> refseq, entrezg, ug respectively
>
> >>>> Thank you very much.
>
> >>>> -Yiwen Chen
>
> >>> ------------------------------
> >>> Mark Robinson, PhD (Melb)
> >>> Epigenetics Laboratory, Garvan
> >>> Bioinformatics Division, WEHI
> >>> e: m.robin...@garvan.org.au
> >>> e: mrobin...@wehi.edu.au
> >>> p: +61 (0)3 9345 2628
> >>> f: +61 (0)3 9347 0852
> >>> ------------------------------
>
> ------------------------------
> Mark Robinson, PhD (Melb)
> Epigenetics Laboratory, Garvan
> Bioinformatics Division, WEHI
> e: m.robin...@garvan.org.au
> e: mrobin...@wehi.edu.au
> p: +61 (0)3 9345 2628
> f: +61 (0)3 9347 0852
> ------------------------------
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